printPairwiseAlignment: Print pairwise alignments of DNA or AA to console or txt file

In Close-your-eyes/igsc: Immunoglobolin sequences from scRNAseq

Print pairwise alignments of DNA or AA to console or txt file

Description

Print pairwise alignments of DNA or AA to console or txt file

Usage

printPairwiseAlignment(
  alignments,
  linewidth = 50,
  match_dots = NULL,
  print_pos = T,
  print_pos_end = F,
  use_align_starts = T,
  col_out = T,
  extend_subject = c(0, 0),
  out_file = NULL
)

Arguments

alignments	one alignment or a list of multiple alignments created with Biostrings::pariwiseAlignment
linewidth	numeric, how many letters of alignment to print per line
match_dots	should matching position be printed as dots for easier recognition of differences; 'subject' to have dots in the subject, 'pattern' to have them in the pattern
print_pos	print the positions of pattern and subject above and below respectively
print_pos_end	print positions on the end of each line
use_align_starts	if TRUE, the first positions are not 1 but refer to position of alignment within the provided sequences
col_out	color the printed alignment?
extend_subject	extend subject further than alignment limits (-,+)
out_file	path to a file where to print results to; if NULL results are printed in console

Value

alignment in printed format in console or file

Close-your-eyes/igsc documentation built on Jan. 28, 2024, 10:28 p.m.